Ok, it's related to Adaptive Sampler Noise Threshold, and seems like a bug. Disabling it or changing the thrasholdthreshold to extremly small values fixed the issue. Noise level on bake doesn't look like the level I set. The difference between pixels on the noise regions of the refence images is a lot bigger than 0.001. It works a lot better on older versions like 2.9. I'm creating bug report at developers portal.